Novoalign: Difference between revisions

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__NOTOC__
__NOTOC__
__NOEDITSECTION__
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[[Category:Software]][[Category:Bioinformatics]]
[[Category:Software]][[Category:Biology]][[Category:NGS]]
<!-- ########  Template Configuration ######## -->
{|<!--Main settings - REQUIRED-->
<!--Edit definitions of the variables used in template calls
Required variables:
app - lowercase name of the application e.g. "amber"
url - url of the software page (project, company product, etc) - e.g. "http://ambermd.org/"
Optional variables:
INTEL - Version of the Intel Compiler e.g. "11.1"
MPI - MPI Implementation and version e.g. "openmpi/1.3.4"
-->
{|
<!--Main settings - REQUIRED-->
|{{#vardefine:app|novoalign}}
|{{#vardefine:app|novoalign}}
|{{#vardefine:url|http://www.novocraft.com/main/page.php?s=novoalign}}
|{{#vardefine:url|http://www.novocraft.com/main/page.php?s=novoalign}}
<!--Compiler and MPI settings - OPTIONAL -->
|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
<!--Choose sections to enable - OPTIONAL-->
|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
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requested by the software manufacturer [http://www.novocraft.com/wiki/tiki-view_faq.php?faqId=1#q23 in Novoalign FAQ].
requested by the software manufacturer [http://www.novocraft.com/wiki/tiki-view_faq.php?faqId=1#q23 in Novoalign FAQ].


==Available versions==
<!--Modules-->
* 2.07.15 - free version (academic, non-profit use; limited functionality and performance)
==Required Modules==
<!-- -->
[[Modules|modules documentation]]
{{#if: {{#var: mod}}|==Running the application using modules==
===Serial===
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
*{{#var:app}}
'''Note:''' Multiple software packages are made available via the novoalign module: novocraft (Novoalign), novoalignCS, novomethyl, and novosort.
===Parallel (MPI)===
* intel
* openmpi
*{{#var:app}}
 
'''Note:''' Multiple software packages are made available via the novoalign module: novoalignMPI and novoalignCSMPI.
 
==System Variables==
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* HPC_NOVOALIGN_BIN - executable directory
* HPC_NOVOALIGN_BIN - executable directory
* HPC_NOVOALIGN_DOC - documentation directory
* HPC_NOVOALIGN_DOC - documentation directory
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{{#if: {{#var: pbs}}|==PBS Script Examples==
{{#if: {{#var: pbs}}|==PBS Script Examples==
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
{{#if: {{#var: policy}}|==Usage policy==
{{#if: {{#var: policy}}|==Usage Policy==
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
{{#if: {{#var: testing}}|==Performance==
{{#if: {{#var: testing}}|==Performance==
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WRITE CITATION HERE
WRITE CITATION HERE
|}}
|}}
=Validation=
* Validated 4/5/2018

Latest revision as of 17:19, 19 August 2022

Description

novoalign website  

Novoalign is a highly accurate program for mapping next-generation sequencing reads to a reference database. It is an aligner for single-ended and paired-end reads from the Illumina Genome Analyser. Novoalign finds global optimum alignments using full Needleman-Wunsch algorithm with affine gap penalties.

Limited functionality and single-threaded performance are available without a paid license. Novoalign must only be used for academic/non-profit research and the results of the analyses must published in peer-reviewed journals as requested by the software manufacturer in Novoalign FAQ.

Required Modules

modules documentation

Serial

  • novoalign

Note: Multiple software packages are made available via the novoalign module: novocraft (Novoalign), novoalignCS, novomethyl, and novosort.

Parallel (MPI)

  • intel
  • openmpi
  • novoalign

Note: Multiple software packages are made available via the novoalign module: novoalignMPI and novoalignCSMPI.

System Variables

  • HPC_NOVOALIGN_DIR - installation directory
  • HPC_NOVOALIGN_BIN - executable directory
  • HPC_NOVOALIGN_DOC - documentation directory




Validation

  • Validated 4/5/2018
Retrieved from "https://help.rc.ufl.edu/mediawiki/index.php?title=Novoalign&oldid=25600"